Identified 20 nodes with invalid xrefs

[cthoyt]

I'm putting together a tool for automatic analysis of the xrefs in a given ontology by using the Bioregistry. When I applied it to UBERON, it identified the following xrefs whose values were not CURIEs. Perhaps when this happens it means it's supposed to be a RO term? It seems to only be getting this issue for relations besides the two entries imported from CL

node_id	xref
http://purl.obolibrary.org/obo/CL_0008047	H3.03.00.0.00012
http://purl.obolibrary.org/obo/CL_4023076	nifext_55
http://purl.obolibrary.org/obo/nbo#by_means	by_means
http://purl.obolibrary.org/obo/nbo#has_participant	has_participant
http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to	anteriorly_connected_to
http://purl.obolibrary.org/obo/uberon/core#channel_for	channel_for
http://purl.obolibrary.org/obo/uberon/core#channels_from	channels_from
http://purl.obolibrary.org/obo/uberon/core#channels_into	channels_into
http://purl.obolibrary.org/obo/uberon/core#conduit_for	conduit_for
http://purl.obolibrary.org/obo/uberon/core#distally_connected_to	distally_connected_to
http://purl.obolibrary.org/obo/uberon/core#filtered_through	filtered_through
http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to	posteriorly_connected_to
http://purl.obolibrary.org/obo/uberon/core#protects	protects
http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to	proximally_connected_to
http://purl.obolibrary.org/obo/uberon/core#subdivision_of	subdivision_of
http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to	transitively_anteriorly_connected_to
http://purl.obolibrary.org/obo/uberon/core#transitively_connected_to	transitively_connected_to
http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to	transitively_distally_connected_to
http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to	transitively_proximally_connected_to
http://www.w3.org/2000/01/rdf-schema#seeAlso	seeAlso

[shawntanzk]

@shawntanzk to look into nifext_55 reference

This comes from https://bioportal.bioontology.org/ontologies/NIFSTD/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_4023076&jump_to_nav=true

@tgbugs - is nifext_55 correct or should it be nifext:55 with nifext meaning something in particular?

[anitacaron]

In the first row, following https://www.wikidata.org/wiki/Q6058407, is H3.03.00.0.00012 a synonym of CL:0008047?

[shawntanzk]

is H3.03.00.0.00012 a synonym of CL:0008047?

guess so lol, maybe change that to exact synonym and add wikidata link as a dbxref AP on the synonym AP

[uberon]

No not a synonym of course, it’s a TH xref missing its prefix I think we should just delete this and auto add all TH, TA xrefs to uberon and cl en masse

…

On Tue, Apr 12, 2022 at 1:49 AM Shawn Tan ***@***.***> wrote: is H3.03.00.0.00012 a synonym of CL:0008047? guess so lol, maybe change that to exact synonym and add wikidata link as a dbxref AP on the synonym AP — Reply to this email directly, view it on GitHub <#2354 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGZRCD7OX6377MNAX7JP7LVEU2KZANCNFSM5Q7Z5HCA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[tgbugs]

NIFEXT:55 expands to http://uri.neuinfo.org/nif/nifstd/nifext_55 and resolves to http://uri.interlex.org/base/ilx_0107375. The prefix rule is @prefix NIFEXT: <http://uri.neuinfo.org/nif/nifstd/nifext_> ..

[anitacaron]

Since the PRs related to this issue were already merged, I'm closing it.

[cthoyt]

@anitacaron i'm not sure if the non-standard relations were issued. I'll start a new issue soon

[anitacaron]

@cthoyt It was solved in this PR #2409